Texture Atlas and Duplicates
I ended up finding a solution that is "elegant" enough to where it would work on even larger scenes where you might have 10-15 copies of multiple objects without being miserable to do. 


First, I dragged a copy of each individual object away from my scene in an area where I'll basically have 1 copy of each unique object. You can even move these on a separate layer if it helps.
Next I grouped up (ctrl+G) all of the objects that are the same within my scene in separate groups. So all the houses in one group, all the trees in one group etc... You can find more properties for grouping under the Object tab (the square icon 3 to the left from Materials)
Using the simple process explained in the video above ( https://www.youtube.com/watch?v=Tj-S5QAac3U ) I created a texture atlas using the unique objects that I've dragged out of my scene. 
Then, I simply went into edit mode and separated all of them out by selection. This is pretty easy to do because I made sure I left some space between them when I dragged the objects away. You just go into edit mode, using B you select the area where your object is and then P and pick by selection.
Next you just pick the groups of objects and the unique object that now has its texture part of an atlas and press ctrl+L to link and link the material and send over the UV mapping too. So for example I would first select the group of houses which has 6 houses that all look exactly the same and then I would select the house that I dragged out to make it my active and then ctrl+L twice to copy the material and UV maps.
The only trick here is that if you want to re-build your atlas at a later point, you need to create new UV maps for all of your unique objects that you've dragged aside. This is simple to do, you just go to the object data tab next to Materials, scroll down to the UV Maps tab, click + to create a new one and delete the old one. Nothing visible will happen when you do this, however if you don't, if you try to join your unique objects with new ones at a later point to try and create a new atlas, your textures will get messed up when you press ctrl+J.


Hope it helps!